[Debichem-devel] Bug#644397: gromacs: pdb2gmx, version 4.5.5, fails with 'Illegal instruction' on i686, 3.0.0.1-686-pae (testing)

groenedraeck groenedraeck at gmail.com
Wed Oct 5 13:37:45 UTC 2011


Package: gromacs
Version: 4.5.5-1
Severity: important

It was found that the pdb2gmx (v4.5.5) from the GROMACS (gromacs v4.5.5-1) fails with an 'Illegal instruction' after the 'Making bonds...' operation (see below).

The bug was first noted in gromacs 4.5.4-2 (bug report not filed, prior versions of gromacs not tested at this workstation), and persists in the recent gromacs 4.5.5-1. In both cases the gromacs packages and all dependencies were installed through aptitude. Although reproducible on a virtual machine (see below), the bug first appeared on a physical computer, equipped with a single 1 GHz AMD Duron processor, 514340k RAM, md0 raid1 controlled by mdadm.

In order to help in locating the source of the problem, all gromacs packages and dependencies were purged from the system. Hereafter, fftw-3.3 was obtained, compiled from source and installed, followed by obtaining, compiling and installing gromacs-4.5.5 from source. The procedure completed according to instructions (c.f. www.gromacs.org - Installation Instructions) and without any errors. However, the pdb2gmx bug was found to be present here also.

On all occasions, the bug was found to be reproducible by following the lysozyme (pdb: 1AKI) GROMACS tutorial (located at http://goo.gl/dxzex). Briefly, the pdb file was obtained, crystal water molecules were removed (two methods have been tried: (i) manual removal of all HOH's in vi; (ii) automatically using CHIMERA), and the resulting 1AKI_waterless.pdb was processed by pdb2gmx using the following command:

$ pdb2gmx -f 1AKI_waterless.pdb -o 1AKI_processed.gro -water spce

This command was executed in a user homedir as well as in /tmp, furthermore the filenames have been varied (w/o underscore, short filename variants), and the '-water spce' directive has also been omitted.

In all cases, the pdb2gmx program starts normally and prompts the user for the force field. Only the following force fields have been tried, but both were found to result in the same illegal instruction:
- 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
-  1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)

The program creates an empty topol.top file and returns to the prompt after displaying:

[..]
Linking CYS-76 SG-601 and CYS-94 SG-724...
Start terminus LYS-1: NH3+
End terminus LEU-129: COO-
Checking for duplicate atoms....
Now there are 129 residues with 1960 atoms
Making bonds...
Illegal instruction
$

I will try to attach the full output to the bugreport.

Furthermore, the bug was found to be reproducable on a virtualbox-ose installation of Debian GNU/Linux testing (Wheezy) i368 (clean install of base system, standard system utilities, gromacs packages and dependencies). In contrary, on an amd64 virtualbox installation of the base system, standard system utilities and gromacs plus all dependencies, the command completes normally without any error. Hence, the bug seems to be i368-specific.

In conclusion, this bug report concerns the pdb2gmx command of gromacs 4.5.5-1, which fails with an 'Illegal instruction' on i368/i686 architectures running Debian GNU/Linux testing (Wheezy) on both a physical computer (1 GHz AMD Duron) as well as on a virtualized vbox i386 installation.


-- System Information:
Debian Release: wheezy/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: i386 (i686)

Kernel: Linux 3.0.0-1-686-pae (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages gromacs depends on:
ii  gromacs-data  4.5.5-1     
ii  libc6         2.13-21     
ii  libfftw3-3    3.2.2-1     
ii  libx11-6      2:1.4.4-2   
ii  libxml2       2.7.8.dfsg-4

Versions of packages gromacs recommends:
ii  cpp  4:4.6.1-2

gromacs suggests no packages.

-- no debconf information

$ dpkg --status gromacs
Package: gromacs
Status: install ok installed
Priority: extra
Section: science
Installed-Size: 13384
Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
Architecture: i386
Version: 4.5.5-1
Depends: gromacs-data (= 4.5.5-1), libc6 (>= 2.7), libfftw3-3, libx11-6, libxml2 (>= 2.7.4)
Recommends: cpp
Breaks: radiance (<= 3R8+20070924.dfsg-1)
Description: Molecular dynamics simulator, with building and analysis tools
 GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
 the Newtonian equations of motion for systems with hundreds to millions of
 particles.
 .
 It is primarily designed for biochemical molecules like proteins and lipids
 that have a lot of complicated bonded interactions, but since GROMACS is
 extremely fast at calculating the nonbonded interactions (that usually
 dominate simulations) many groups are also using it for research on non-
 biological systems, e.g. polymers.
 .
 GROMACS offers entirely too many features for a brief description to do it
 justice.  A more complete listing is available at
 <http://www.gromacs.org/content/view/12/176/>.
Homepage: http://www.gromacs.org/
-------------- next part --------------
$ pdb2gmx -f 1AKI_waterless.pdb -o 1AKI_processed.gro -water spce

                         :-)  G  R  O  M  A  C  S  (-:

               Go Rough??????? Many An???????ese Seri???????rs

                            :-)  VERSION 4.5.5  (-:

        Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
      Aldert van Buuren, P?r Bjelkmar, Rudi van Drunen, Anton Feenstra, 
        Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff, 
           Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, 
                Michael Shirts, Alfons Sijbers, Peter Tieleman,

               Berk Hess, David van der Spoel, and Erik Lindahl.

       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
            Copyright (c) 2001-2010, The GROMACS development team at
        Uppsala University & The Royal Institute of Technology, Sweden.
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                               :-)  pdb2gmx  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -f 1AKI_waterless.pdb  Input        Structure file: gro g96 pdb tpr etc.
  -o 1AKI_processed.gro  Output       Structure file: gro g96 pdb etc.
  -p      topol.top  Output       Topology file
  -i      posre.itp  Output       Include file for topology
  -n      clean.ndx  Output, Opt. Index file
  -q      clean.pdb  Output, Opt. Structure file: gro g96 pdb etc.

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    0       Set the nicelevel
-chainsep    enum   id_or_ter  Condition in PDB files when a new chain should
                  -merge       enum   no      Merge multiple chains into a single
                -ff          string select  Force field, interactive by default. Use -h for
                    -water       enum   spce    Water model to use: select, none, spc, spce,
               -[no]inter   bool   no      Set the next 8 options to interactive
-[no]ss      bool   no      Interactive SS bridge selection
-[no]ter     bool   no      Interactive termini selection, instead of charged
          -[no]lys     bool   no      Interactive lysine selection, instead of charged
-[no]arg     bool   no      Interactive arginine selection, instead of charged
-[no]asp     bool   no      Interactive aspartic acid selection, instead of
            -[no]glu     bool   no      Interactive glutamic acid selection, instead of
            -[no]gln     bool   no      Interactive glutamine selection, instead of
        -[no]his     bool   no      Interactive histidine selection, instead of
                -angle       real   -nan    Minimum hydrogen-donor-acceptor angle for a
                -dist        real   -nan    Maximum donor-acceptor distance for a H-bond (nm)
-[no]una     bool   no      Select aromatic rings with united CH atoms on
              -[no]ignh    bool   no      Ignore hydrogen atoms that are in the coordinate
           -[no]missing bool   no      Continue when atoms are missing, dangerous
-[no]v       bool   no      Be slightly more verbose in messages
-posrefc     real   -nan    Force constant for position restraints
-vsite       enum   none    Convert atoms to virtual sites: none, hydrogens
                    -[no]heavyh  bool   no      Make hydrogen atoms heavy
-[no]deuterate bool no      Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes     Use charge groups in the .rtp file
-[no]cmap    bool   yes     Use cmap torsions (if enabled in the .rtp file)
-[no]renum   bool   no      Renumber the residues consecutively in the output
-[no]rtpres  bool   no      Use .rtp entry names as residue names


Select the Force Field:
>From '/usr/share/gromacs/top':
 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
 2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
 3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
 4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
 5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
 7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
 8: CHARMM27 all-atom force field (with CMAP) - version 2.0
 9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR

14

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading 1AKI_waterless.pdb...
WARNING: all CONECT records are ignored
Read 'LYSOZYME', 1001 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 129 residues with 1001 atoms

  chain  #res #atoms
  1 'A'   129   1001  

All occupancies are one
Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 56
Sorting it all out...
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.1#
WARNING: unsupported proton mass multiplier (-nan) in pdb2top
Processing chain 1 'A' (1001 atoms, 129 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
 protonation. 213 donors and 184 acceptors were found.
There are 254 hydrogen bonds
Will use HISE for residue 15
Identified residue LYS1 as a starting terminus.
Identified residue LEU129 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
                    CYS6   MET12   HIS15   CYS30   CYS64   CYS76   CYS80
                    SG48    SD87  NE2118   SG238   SG513   SG601   SG630
   MET12    SD87   1.166
   HIS15  NE2118   1.776   1.019
   CYS30   SG238   1.406   1.054   2.069
   CYS64   SG513   2.835   1.794   1.789   2.241
   CYS76   SG601   2.704   1.551   1.468   2.116   0.765
   CYS80   SG630   2.959   1.951   1.916   2.391   0.199   0.944
   CYS94   SG724   2.550   1.407   1.382   1.975   0.665   0.202   0.855
  MET105   SD799   1.827   0.911   1.683   0.888   1.849   1.461   2.036
  CYS115   SG889   1.576   1.084   2.078   0.200   2.111   1.989   2.262
  CYS127   SG981   0.197   1.072   1.721   1.313   2.799   2.622   2.934
                   CYS94  MET105  CYS115
                   SG724   SD799   SG889
  MET105   SD799   1.381
  CYS115   SG889   1.853   0.790
  CYS127   SG981   2.475   1.686   1.483
Linking CYS-6 SG-48 and CYS-127 SG-981...
Linking CYS-30 SG-238 and CYS-115 SG-889...
Linking CYS-64 SG-513 and CYS-80 SG-630...
Linking CYS-76 SG-601 and CYS-94 SG-724...
Start terminus LYS-1: NH3+
End terminus LEU-129: COO-
Checking for duplicate atoms....
Now there are 129 residues with 1960 atoms
Making bonds...
Illegal instruction

$
-------------- next part --------------
processor	: 0
vendor_id	: AuthenticAMD
cpu family	: 6
model		: 7
model name	: AMD Duron(tm) processor
stepping	: 0
cpu MHz		: 1001.722
cache size	: 64 KB
fdiv_bug	: no
hlt_bug		: no
f00f_bug	: no
coma_bug	: no
fpu		: yes
fpu_exception	: yes
cpuid level	: 1
wp		: yes
flags		: fpu vme de pse tsc msr pae mce cx8 sep mtrr pge mca cmov pat pse36 mmx fxsr sse syscall mmxext 3dnowext 3dnow up
bogomips	: 2003.44
clflush size	: 32
cache_alignment	: 32
address sizes	: 34 bits physical, 32 bits virtual
power management: ts



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